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kevlar-dev / kevlar

Reference-free variant discovery in large eukaryotic genomes
https://kevlar.readthedocs.io
MIT License
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Reimplement varfilter #345

Closed standage closed 5 years ago

standage commented 5 years ago

The number of variant predictions is dwarfed by the number of common variants, segdups, and SSRs to mask. Rather than storing the regions to mask in an interval forest, store the predictions and query the using the regions to mask.

Probably want to add a flag to the variant.annotate() method to overwrite instead of append an INFO value.

standage commented 5 years ago

See #351 regarding new behavior or variant.annotate().